Publications by Nasir Mahmood Abbasi
Harmony Integration_Test1
1. load libraries 2. Load Seurat Object #Load Seurat Object merged from cell lines and a control(PBMC) after filtration SS_All_samples_Merged <- load("SS_All_Sample_Merged_Azimuth_ProjectTils_singleR_ANNOTATION_on_My_UMAP0.7_HPC.Robj") All_samples_Merged An object of class Seurat 63193 features across 49193 samples within 6 assays Active assay...
6534 sym Python (4695 sym/25 pcs) 17 img
CCA_harmony_0.5
1. load libraries 2. Load Seurat Object load("AllSample_corrected_AzimuthAnnotated_L1.Robj") All_samples_Merged 3. Data PREPERATION alldata <- All_samples_Merged alldata.list <- SplitObject(alldata, split.by = "orig.ident") for (i in 1:length(alldata.list)) { alldata.list[[i]] <- NormalizeData(alldata.list[[i]], verbose = FALSE) alld...
17545 sym Python (16107 sym/46 pcs) 34 img
CCA-Harmony_new
1. load libraries 2. Load Seurat Object load("AllSample_corrected_AzimuthAnnotated_L1.Robj") All_samples_Merged An object of class Seurat 36724 features across 49193 samples within 5 assays Active assay: RNA (36601 features, 0 variable features) 2 layers present: counts, data 4 other assays present: ADT, prediction.score.celltype.l1, predict...
17127 sym Python (10265 sym/35 pcs) 35 img
rpca-Harmony_new
1. load libraries 2. Load Seurat Object load("AllSample_corrected_AzimuthAnnotated_L1.Robj") All_samples_Merged 3. Data PREPERATION alldata <- All_samples_Merged alldata.list <- SplitObject(alldata, split.by = "orig.ident") for (i in 1:length(alldata.list)) { alldata.list[[i]] <- NormalizeData(alldata.list[[i]], verbose = FALSE) alld...
8723 sym Python (1817 sym/5 pcs) 4 img
Integration-Harmony
1. load libraries 2. Load Seurat Object load("../5-SS_ScRNA_Data_Analysis/4-ScSS_MyAnalysis_on_SS/2-Marie-Objects-Merged-into-Seurat-Object/1-Merged_using_marie_obj/SS_merged_marie_obj-2-Variation.Robj") #Load Seurat Object merged from cell lines and a control(PBMC) after filtration load("../5-SS_ScRNA_Data_Analysis/4-ScSS_MyAnalysis_on_SS/5-HPC...
5909 sym Python (9450 sym/18 pcs) 3 img
rpca-Integration
1. load libraries 2. Load Seurat Object #Load Seurat Object merged from cell lines and a control(PBMC) after filtration load("../5-SS_ScRNA_Data_Analysis/4-ScSS_MyAnalysis_on_SS/2-Marie-Objects-Merged-into-Seurat-Object/1-Merged_using_marie_obj/SS_merged_marie_obj-2-Variation.Robj") All_samples_Merged An object of class Seurat 36629 features ac...
6310 sym Python (13877 sym/82 pcs) 4 img
Integration-CCA
1. load libraries 2. Load Seurat Object #Load Seurat Object merged from cell lines and a control(PBMC) after filtration load("../5-SS_ScRNA_Data_Analysis/4-ScSS_MyAnalysis_on_SS/2-Marie-Objects-Merged-into-Seurat-Object/1-Merged_using_marie_obj/SS_merged_marie_obj-2-Variation.Robj") All_samples_Merged An object of class Seurat 36629 features ac...
6092 sym Python (14051 sym/80 pcs) 4 img
Corrected-UMAP
1. load libraries 2. Load Seurat Object #Load Seurat Object merged from cell lines and a control(PBMC) after filtration load("AllSample_corrected.Robj") AllSample An object of class Seurat 38620 features across 49193 samples within 3 assays Active assay: integrated (1991 features, 1991 variable features) 2 layers present: data, scale.data 2 ...
6232 sym Python (5525 sym/29 pcs) 6 img
integration by Different Methods-rpca-CCA-Harmony
1. load libraries 2. Load Seurat Object #Load Seurat Object merged from cell lines and a control(PBMC) after filtration load("SS_merged_marie_obj-2-Variation.Robj") All_samples_Merged An object of class Seurat 36629 features across 49193 samples within 2 assays Active assay: RNA (36601 features, 0 variable features) 2 layers present: counts, ...
11408 sym Python (13614 sym/86 pcs) 7 img
Testing Integration: CCA, Harmony
load libraries 1. Load Seurat Object #Load Seurat Object merged from cell lines and a control(PBMC) after filtration load("SS_All_Sample_Merged_Azimuth_ProjectTils_singleR_ANNOTATION_on_My_UMAP0.7_HPC.Robj") All_samples_Merged An object of class Seurat 63193 features across 49193 samples within 6 assays Active assay: SCT (26469 features, 3000 ...
8168 sym Python (34510 sym/89 pcs) 13 img